title: Profiling deacetylase activities in cell lysates with peptide arrays and SAMDI mass spectrometry.
abstract: The development of arrays that can profile molecular activities in cells is important to understanding signaling pathways in normal and pathological settings. While oligonucleotide arrays are now routinely used to profile global gene expression, there is still a lack of tools for profiling enzyme activities in cell lysates. This paper describes the combination of peptide arrays formed on self-assembled monolayers and mass spectrometry to provide a label-free approach for identifying patterns of enzyme activities in cell lysates. The approach is demonstrated by profiling lysine deacetylase (KDAC) activities in cell lysates of the CHRF megakaryocytic (Mk) cell line. Class-specific deacetylase inhibitors were used to show that terminal Mk differentiation of CHRF cells is marked by a pronounced decrease in sirtuin activity and by little change in activity of KDACs 1-11. This work establishes a platform that can be used to identify changes in global activity profiles of cell lysates for a wide variety of enzymatic activities.
authors.affiliation: Departments of Biomedical Engineering, Chemistry, Cell & Molecular Biology, Northwestern University, Evanston, Illinois 60208.
authors.forename: Hsin-Yu
authors.initials: HY
authors.lastname: Kuo
authors.affiliation: Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208.
authors.forename: Teresa A
authors.initials: TA
authors.lastname: DeLuca
authors.affiliation: Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208.|Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611.
authors.forename: William M
authors.initials: WM
authors.lastname: Miller
authors.affiliation: Departments of Biomedical Engineering, Chemistry, Cell & Molecular Biology, Northwestern University, Evanston, Illinois 60208.|Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611.
authors.forename: Milan
authors.initials: M
authors.lastname: Mrksich
mesh_terms: D000107:Acetylation; D015153:Blotting, Western; D002478:Cells, Cultured; D005434:Flow Cytometry; D006655:Histone Deacetylases / Q000378:metabolism*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008533:Megakaryocytes / Q000166:cytology / Q000378:metabolism*; D010446:Peptide Fragments / Q000032:analysis*; D019151:Peptide Library; D040081:Protein Array Analysis; D015398:Signal Transduction; D013379:Substrate Specificity
chemical_list: D010446:Peptide Fragments; D019151:Peptide Library; D006655:Histone Deacetylases